title: Normal tissue for ID_048

description: no additional information

tag: Patient_ID = ID_048

tag: Sex = F

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No


title: Cancer tissue for ID_050

status: Public on Aug 21 2008

type: genomic

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

country: Japan

institute: Jichi Medical University

description: no additional information

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner 3000, GCOS 1.2

data_processing: DAT and CEL files were processed by Affymetrix GCOS 1.2 with default analysis settings. Calls generated by GDAS 3.0 with confidence threshold 0.05.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal tissue

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA with high molecular weight was performed using QIamp micro DNA extraction kit (Qiagen, Valencia, CA) following the manufacturer's instructions.

tag: disease_state = Carcinoma

tag: Patient_ID = ID_050

tag: Sex = M

tag: MSI = No

tag: Observation_(days) = 1505

tag: Censor = Yes


title: Normal tissue for ID_039

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_039

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 932

tag: Censor = No


title: Cancer tissue for ID_040

description: no additional information

tag: Patient_ID = ID_040

tag: Position = Right

tag: Observation_(days) = 162


title: Cancer tissue for ID_045

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_045

tag: Pathology = mucinous adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1365


title: Normal tissue for ID_038

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_038

tag: Sex = M

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: MSI = No

tag: Observation_(days) = 1546

tag: Censor = Yes


title: Cancer tissue for ID_038

description: no additional information


title: Normal tissue for ID_042

description: no additional information

tag: Patient_ID = ID_042

tag: Position = Rectum

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1537


title: Cancer tissue for ID_042

description: no additional information

tag: disease_state = Carcinoma


title: Cancer tissue for ID_039

description: no additional information

tag: Patient_ID = ID_039

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 932

tag: Censor = No


title: Normal tissue for ID_040

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_040

tag: Position = Right

tag: Observation_(days) = 162


title: Normal tissue for ID_035

description: no additional information

tag: Patient_ID = ID_035

tag: Sex = M

tag: Pathology = poorly differentiated adenocarcinoma

tag: Duke's_grade = D

tag: MSI = No

tag: Observation_(days) = 520


title: Cancer tissue for ID_036

description: no additional information

tag: Patient_ID = ID_036

tag: Sex = F

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1558

tag: Censor = Yes


title: Normal tissue for ID_037

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_037

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1554


title: Cancer tissue for ID_037

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = M


title: Normal tissue for ID_031

description: no additional information

tag: Patient_ID = ID_031

tag: Age = 52

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: MSI = No

tag: Observation_(days) = 864

tag: Censor = No


title: Cancer tissue for ID_035

description: no additional information

tag: Patient_ID = ID_035

tag: Pathology = poorly differentiated adenocarcinoma

tag: Duke's_grade = D

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 520


title: Normal tissue for ID_036

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_036

tag: Sex = F

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Observation_(days) = 1558

tag: Censor = Yes


title: Normal tissue for ID_032

description: no additional information

tag: Patient_ID = ID_032

tag: Position = Rectum

tag: Observation_(days) = 880


title: muscle_young_APB_3

type: RNA

city: Urbana

first: Kelly

middle: Scott

last: Swanson

state: IL

address: 1207 W. Gregory Dr.

country: USA

institute: University of Illinois

description: Gene expression data from skeletal muscle of 1 yr-old dogs after 1 yr on APB diet

hyb_protocol: Purified, fragmented cRNA was hybridized to Affymetrix's Canine Genome Array (version 1) using Affymetrix's GeneChip Fluidics Station 450, as per Affymetrix's instructions.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000

data_processing: Pre-processing was done using the GCRMA algorithm in R and Bioconductor packages. Additionally, Affymetrix's Call Detection algorithm was used to exclude probesets that were not called Present on at least one array or Marginal on two arrays from differential analysis.

molecule: total RNA

organism: Canis lupus familiaris

source_name: Skeletal muscle at 1 yr, after 1 year on APB diet

label_protocol: Biotin-labeled cRNA samples were made using Affymetrix GeneChip  Expression 3'-Amplification Reagents (One-Cycle Target Labeling and Control Reagents package) according to the manufacturer's instructions.

growth_protocol: Young dogs (mean age = 8 wk at baseline) were fed ad libitum throughout the study to allow for adequate growth; old dogs (mean age = 11.1 yr at baseline) were fed to maintain baseline BW.

extract_protocol: Total RNA was extracted using Trizol as suggested by the manufacturer.

treatment_protocol: Dogs were allotted to 1 of 2 diets and fed for 12 months: 1) animal-protein based (APB) diet primarily composed of highly digestible, animal-derived ingredients and formulated to exceed protein and fat recommendations provided by the Association of American Feed Control Officials (AAFCO) for growth and reproduction; or 2) plant-protein based (PPB) diet primarily composed of moderately digestible, plant-derived ingredients and formulated to meet protein and fat recommendations for growth and reproduction by AAFCO.  The exception was 10% meat and bone meal in the diet.  All samples were collected after an overnight food-restricted period.

tag: Tissue

value: Skeletal muscle

tag: Age

value: 1 yr

tag: Diet

value: Animal-Protein Based

tag: Breed

value: Beagle


title: Cancer tissue for ID_032

description: no additional information

tag: disease_state = Carcinoma

tag: Lymph_node_metastasis = Yes

tag: MSI = No

tag: Censor = No


title: Normal tissue for ID_030

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_030

tag: Sex = F

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = A

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1581


title: Cancer tissue for ID_028

description: no additional information

tag: Patient_ID = ID_028

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Observation_(days) = 1588

tag: Censor = Yes


title: Normal tissue for ID_028

description: no additional information


title: muscle_young_PPB_2

description: Gene expression data from skeletal muscle of 1 yr-old dogs after 1 yr on PPB diet

source_name: Skeletal muscle at 1 yr, after 1 year on PPB diet

tag: Tissue

tag: Age

tag: Diet

value: Plant-Protein Based

tag: Breed


title: Cancer tissue for ID_030

description: no additional information

tag: disease_state = Carcinoma

tag: Position = Rectum

tag: MSI = No


title: Cancer tissue for ID_031

description: no additional information

tag: Patient_ID = ID_031

tag: Age = 52

tag: Sex = M

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 864

tag: Censor = No


title: Normal tissue for ID_034

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_034

tag: Pathology = well differentiated adenocarcinoma

tag: Lymph_node_metastasis = No

tag: Observation_(days) = 1561


title: Cancer tissue for ID_034

description: no additional information

tag: Duke's_grade = B

tag: Censor = Yes


title: muscle_young_PPB_3

tag: Tissue

tag: Age

tag: Diet

tag: Breed


title: muscle_young_APB_2


title: muscle_old_PPB_3

description: Gene expression data from skeletal muscle of 12 yr-old dogs after 1 yr on PPB diet

source_name: Skeletal muscle at 12 yrs, after 1 year on PPB diet

value: 12 yrs


title: Cancer tissue for ID_027

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_027

tag: Position = Left

tag: MSI = No

tag: Observation_(days) = 1145


title: Normal tissue for ID_027

description: no additional information

tag: Sex = M

tag: Censor = No


title: Normal tissue for ID_026

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_026

tag: Sex = F

tag: Position = Right

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1589


title: Cancer tissue for ID_026

description: no additional information

tag: Pathology = well differentiated adenocarcinoma

tag: Censor = Yes


title: muscle_young_PPB_1

tag: Tissue

tag: Age

tag: Diet

tag: Breed


title: Normal tissue for ID_025

description: no additional information

tag: Patient_ID = ID_025

tag: Position = Left

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1595


title: muscle_old_PPB_2


title: muscle_old_APB_3

description: Gene expression data from skeletal muscle of 12 yr-old dogs after 1 yr on APB diet

source_name: Skeletal muscle at 12 yrs, after 1 year on APB diet


title: A9 anoxic YEM 7

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: B. japonicum nifA mutant grown anoxically

hyb_protocol: Modification of Affymetrix protocol used for Pseudomonas aeruginosa

scan_protocol: Standard Affymetrix procedures

data_processing: GeneChip Operating Software (GCOS) version 1.2 (Affymetrix)

organism: Bradyrhizobium japonicum

label_protocol: 2.2 ug (culture-grown bacteria) and 5.5-8 ug (nodules) cDNA were labeled with biotin

growth_protocol: Cells were grown to mid-exponential phase which corresponded to an OD600 of 0.4 to 0.5 in microoxic cultures (PSY-arabinose medium) and a OD600 of 0.175 to 0.225 in anoxic cultures (YEM-nitrate medium); soybean nodules were harvested 21 days post inoculation (dpi)

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

tag: Genotype

tag: Growth condition

value: anoxic

tag: Medium

value: YEM


title: Cancer tissue for ID_025

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = F


title: A9 anoxic YEM 4

source_name: B. japonicum nifA mutant grown anoxically


title: muscle_old_APB_2


title: A9 anoxic YEM 5


title: A9 anoxic YEM 3


title: A9 anoxic YEM 6


title: A9 anoxic YEM 2


title: muscle_old_APB_1


title: muscle_young_APB_1


title: Cancer tissue for ID_024

description: no additional information

tag: Patient_ID = ID_024

tag: Sex = M

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1596


title: A9 anoxic YEM 1


title: muscle_old_PPB_1

tag: Tissue

tag: Age

tag: Diet


title: 7454 anoxic YEM 6

description: B. japonicum fixK1 mutant grown anoxically


title: 7360 nodules soybean 21 Days 3

description: nodules soybean 21 dpi infected by a B. japonicum fixJ mutant

source_name: nodules soybean 21 dpi infected by B. japonicum fixJ mutant

value: nodules

value: soybean


title: 9043 nodules soybean 21 Days 3

description: nodules soybean 21 dpi infected by a B. japonicum fixK2 mutant

source_name: nodules soybean 21 dpi infected by B. japonicum fixK2 mutant


title: Cancer tissue for ID_023

description: no additional information

tag: Patient_ID = ID_023

tag: Position = Right

tag: Observation_(days) = 1599

tag: Censor = Yes


title: 9043 nodules soybean 21 Days 2


title: SCA3_NS31

city: Leiden

first: Jan

last: Oosting

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix focus arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data files of all arrays were normalized using sequence information in Robust Multi_Chip Average (GCRMA) method.

source_name: SCA3, patient 91d

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: Gender

value: Female

value: Serous ovary tumor

tag: Classification

value: Carcinoma grade 3


title: SBT_NS36

description: Gene expression data

source_name: SBT, patient 82

value: Borderline tumor


title: Normal tissue for ID_023

description: no additional information

tag: disease_state = Normal

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No


title: 7360 nodules soybean 21 Days 2

tag: Genotype

tag: Growth condition

tag: Medium


title: MPC_NS13

description: Gene expression data

source_name: MPC, patient 81

value: Micropapillary carcinoma


title: 7360 nodules soybean 21 Days 1


title: 9043 nodules soybean 21 Days 1


title: Cancer tissue for ID_022

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_022

tag: Sex = M

tag: Pathology = well differentiated adenocarcinoma

tag: MSI = Yes

tag: Observation_(days) = 1601


title: 7454 anoxic YEM 5

source_name: B. japonicum fixK1 mutant grown anoxically


title: Normal tissue for ID_024

description: no additional information

tag: Patient_ID = ID_024

tag: Position = Left

tag: Observation_(days) = 1596


title: Normal tissue for ID_022

description: no additional information

tag: Position = Right

tag: Censor = Yes


title: SCA3_NS61

description: Gene expression data

source_name: SCA3, patient 73

tag: Gender

tag: Tissue

tag: Classification


title: MPC_NS17

description: Gene expression data

source_name: MPC, patient 50


title: 7454 anoxic YEM 4


title: 7454 anoxic YEM 3


title: Cancer tissue for ID_021

description: no additional information

tag: Patient_ID = ID_021

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No


title: Normal tissue for ID_020

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_020

tag: Age = 78

tag: Sex = F

tag: Pathology = poorly differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 43

tag: Censor = No


title: SCA3_NS22

description: Gene expression data

source_name: SCA3, patient 46


title: Normal tissue for ID_021

description: no additional information

tag: Sex = M

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Observation_(days) = 1601

tag: Censor = Yes


title: SCA3_NS19

description: Gene expression data

source_name: SCA3, patient 27

tag: Gender

tag: Tissue

tag: Classification


title: 110spc4 anoxic YEM 12

description: B. japonicum wild-type strain grown anoxically

tag: Genotype

tag: Growth condition

tag: Medium


title: 7454 anoxic YEM 1


title: Normal tissue for ID_018

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_018

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = Yes

tag: Observation_(days) = 1613


title: Cancer tissue for ID_020

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_020

tag: Age = 78

tag: Sex = F

tag: Pathology = poorly differentiated adenocarcinoma

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 43

tag: Censor = No


title: SCA3_NS07

description: Gene expression data

source_name: SCA3, patient 40

tag: Gender

tag: Tissue

tag: Classification


title: SCA3_NS51

description: Gene expression data

source_name: SCA3, patient 251


title: 110spc4 anoxic YEM 13

source_name: B. japonicum wild-type strain grown anoxically

tag: Genotype

tag: Growth condition

tag: Medium


title: SBT_NS33

description: Gene expression data

source_name: SBT, patient 7


title: 7454 anoxic YEM 2


title: stg 3d TA_1

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: stg 3d TA_1

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

organism: Mus musculus

source_name: stg 3d TA cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNeasy

treatment_protocol: in vitro stimulated

tag: genetic modification

value: TCR-HA

tag: tissue

value: Spleen


title: Cancer tissue for ID_018

description: no additional information

source_name: Colorectal tissue

tag: disease_state = Carcinoma

tag: Patient_ID = ID_018

tag: Sex = M

tag: Position = Right

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = Yes

tag: Observation_(days) = 1613

tag: Censor = Yes


title: 110spc4 anoxic YEM 9


title: 110spc4 anoxic YEM 11


title: stg 3d TA_3

description: stg 3d TA_3


title: 110spc4 anoxic YEM 10


title: WT TR_3

description: WT TR_3

source_name: wild-type (WT) TR cells

tag: genetic modification:


title: stg 3d TA_2

description: stg 3d TA_2


title: SCA1_NS43

description: Gene expression data

source_name: SCA1, patient 249

tag: Gender

tag: Tissue

value: Carcinoma grade 1


title: Normal tissue for ID_017

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_017

tag: Position = Rectum

tag: Pathology = moderately differentiated adenocarcinoma

tag: Duke's_grade = D

tag: Lymph_node_metastasis = Yes

tag: MSI = No

tag: Observation_(days) = 760

tag: Censor = No


title: Cancer tissue for ID_017

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = M


title: SCA1_NS29

description: Gene expression data

source_name: SCA1, patient 246

tag: Classification


title: WT TR_2

description: WT TR_2

tag: tissue


title: SBT_NS28

description: Gene expression data

source_name: SBT, patient 244


title: SBT_NS34

description: Gene expression data

source_name: SBT, patient 245


title: Normal tissue for ID_016

description: no additional information

tag: Patient_ID = ID_016

tag: Age = 70

tag: Sex = F

tag: Position = Right

tag: Pathology = mucinous adenocarcinoma

tag: Duke's_grade = C

tag: MSI = Yes

tag: Observation_(days) = 1616

tag: Censor = Yes


title: Cancer tissue for ID_016

description: no additional information

tag: Lymph_node_metastasis = Yes


title: 110spc4 anoxic YEM 5

tag: Genotype

tag: Growth condition

tag: Medium


title: WT TR_1

description: WT TR_1

tag: genetic modification:


title: 110spc4 anoxic YEM 6


title: stg TR_3

description: stg TR_3

source_name: stg TR cells

tag: genetic modification


title: 110spc4 anoxic YEM 7


title: 110spc4 anoxic YEM 8


title: SCA3_NS50

description: Gene expression data

source_name: SCA3, patient 243

tag: Gender

tag: Tissue

tag: Classification


title: Normal tissue for ID_015

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_015

tag: Sex = M

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1617


title: stg TN_3

description: stg TN_3

source_name: stg TN cells

tag: tissue


title: SBT_NS27

description: Gene expression data

source_name: SBT, patient 242


title: stg TR_2

description: stg TR_2


title: stg TR_1

description: stg TR_1


title: Normal tissue for ID_014

description: no additional information

tag: Patient_ID = ID_014

tag: Position = Left

tag: Pathology = moderately differentiated adenocarcinoma

tag: Observation_(days) = 18

tag: Censor = Yes


title: SCA3_NS49

description: Gene expression data

source_name: SCA3, patient 241

tag: Gender

tag: Tissue


title: 110spc4 anoxic YEM 3

tag: Genotype

tag: Growth condition

tag: Medium


title: 110spc4 anoxic YEM 4


title: SCA3_NS35

description: Gene expression data

source_name: SCA3, patient 240

tag: Classification


title: Cancer tissue for ID_014

description: no additional information

tag: disease_state = Carcinoma

tag: Sex = M


title: 110spc4 anoxic YEM 2


title: stg TN_1

description: stg TN_1

tag: genetic modification


title: Cancer tissue for ID_015

description: no additional information

tag: Patient_ID = ID_015

tag: Position = Rectum

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No


title: SCA3_NS25

description: Gene expression data

source_name: SCA3, patient 239b


title: SCA1_NS30

description: Gene expression data

source_name: SCA1, patient 229


title: stg TN_2

description: stg TN_2

tag: tissue


title: 110spc4 anoxic YEM 1

source_name: B. japonicum wild-type strain grown anoxically


title: dtg CD25+ TR_3

description: dtg CD25+ TR_3

source_name: dtg CD25+ TR cells

value: TCR-HA x Ig-HA


title: 7454 microaerobiosis PSY 6

description: B. japonicum fixK1 mutant grown microaerobically

value: microaerobiosis

value: PSY


title: dtg CD25+ TR_2

description: dtg CD25+ TR_2


title: Cancer tissue for ID_013

description: no additional information

tag: Patient_ID = ID_013

tag: Sex = F

tag: Position = Left

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 510

tag: Censor = No


title: dtg CD25+ TR_1

description: dtg CD25+ TR_1


title: dtg CD25- TR_3

description: dtg CD25- TR_3

source_name: dtg CD25- TR cells


title: Normal tissue for ID_013

description: no additional information

source_name: Colorectal tissue

tag: disease_state = Normal


title: Cancer tissue for ID_012

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_012

tag: Sex = M

tag: Observation_(days) = 1624

tag: Censor = Yes


title: SBT_NS01

description: Gene expression data

source_name: SBT, patient 220

tag: Gender

tag: Tissue

tag: Classification


title: 7454 microaerobiosis PSY 4

source_name: B. japonicum fixK1 mutant grown microaerobically

tag: Growth condition

tag: Medium


title: 7454 microaerobiosis PSY 5


title: Impl_NS46

description: Gene expression data

source_name: Implant, patient 206

value: Implant


title: SCA1_NS38

description: Gene expression data

source_name: SCA1, patient 221


title: dtg CD25- TR_2

description: dtg CD25- TR_2

tag: genetic modification

tag: tissue


title: Cancer tissue for ID_010

description: no additional information

tag: Patient_ID = ID_010

tag: Sex = F

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1133


title: 7454 microaerobiosis PSY 1


title: SBT_NS24

description: Gene expression data

source_name: SBT, patient 195


title: Normal tissue for ID_012

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_012

tag: Sex = M

tag: Position = Rectum

tag: Observation_(days) = 1624


title: dtg CD25- TR_1

description: dtg CD25- TR_1


title: SBT_NS18

description: Gene expression data

source_name: SBT, patient 2

tag: Gender

tag: Tissue

tag: Classification


title: Normal tissue for ID_009

description: no additional information

tag: Patient_ID = ID_009

tag: Observation_(days) = 1635

tag: Censor = Yes


title: 7454 microaerobiosis PSY 2

tag: Growth condition

tag: Medium


title: Normal tissue for ID_010

description: no additional information

tag: Patient_ID = ID_010

tag: Sex = F

tag: Position = Left

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B


title: 9043 microaerobiosis PSY 8

description: B. japonicum fixK2 mutant grown microaerobically

tag: Genotype


title: stg 16h TA_3

description: stg 16h TA_3

source_name: in vitro-stimulated stg 16h TA cells

tag: genetic modification

tag: tissue


title: 7454 microaerobiosis PSY 3


title: SCA3_NS15

description: Gene expression data

source_name: SCA3, patient 187


title: SCA1_NS26

description: Gene expression data

source_name: SCA1, patient 181


title: stg 16h TA_2

description: stg 16h TA_2


title: SCA1_NS06

description: Gene expression data

source_name: SCA1, patient 180


title: SCA3_NS32

description: Gene expression data

source_name: SCA3, patient 179


title: Normal tissue for ID_008

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_008

tag: Sex = M

tag: Position = Rectum

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1642


title: Cancer tissue for ID_009

description: no additional information

tag: disease_state = Carcinoma

tag: Patient_ID = ID_009

tag: Observation_(days) = 1635

tag: Censor = Yes


title: stg 16h TA_1

description: stg 16h TA_1


title: 9043 microaerobiosis PSY 5

source_name: B. japonicum fixK2 mutant grown microaerobically

tag: Growth condition

tag: Medium


title: Cancer tissue for ID_008

description: no additional information

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B


title: SCA3_NS23

description: Gene expression data

source_name: SCA3, patient 176

tag: Gender

tag: Tissue

tag: Classification


title: 9043 microaerobiosis PSY 6

tag: Genotype


title: Normal tissue for ID_007

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_007

tag: Sex = F

tag: Position = Left

tag: Observation_(days) = 1644


title: 9043 microaerobiosis PSY 4


title: SCA3_NS39

description: Gene expression data

source_name: SCA3, patient 151


title: Cancer tissue for ID_007

description: no additional information

tag: disease_state = Carcinoma

tag: Lymph_node_metastasis = No

tag: MSI = No


title: Cancer tissue for ID_006

description: no additional information

tag: Patient_ID = ID_006

tag: Position = Rectum

tag: Duke's_grade = C

tag: Lymph_node_metastasis = Yes

tag: Observation_(days) = 1645

tag: Censor = Yes


title: Normal tissue for ID_006

description: no additional information

tag: Pathology = well differentiated adenocarcinoma


title: 9043 microaerobiosis PSY 3

tag: Growth condition

tag: Medium


title: SCA3_NS11

description: Gene expression data

source_name: SCA3, patient 154

tag: Gender

tag: Tissue

tag: Classification


title: 9043 microaerobiosis PSY 2

tag: Genotype


title: SCA1_NS21

description: Gene expression data

source_name: SCA1, patient 171


title: 9043 microaerobiosis PSY 7


title: 7360 microaerobiosis PSY 6

description: B. japonicum fixJ mutant grown microaerobically


title: 9043 microaerobiosis PSY 1


title: Normal tissue for ID_005

description: no additional information

source_name: Colorectal tissue

tag: disease_state = Normal

tag: Patient_ID = ID_005

tag: Sex = F

tag: MSI = Yes

tag: Observation_(days) = 957

tag: Censor = No


title: Cancer tissue for ID_005

description: no additional information

tag: disease_state = Carcinoma

tag: Position = Rectum

tag: Duke's_grade = C


title: E. coli 15 minute 5 µM cadmium dye swap treatment

city: Oshkosh

first: Craig

last: Worden

state: WI

address: 800 Algoma Boulevard

department: Biology and Microbiology

institute: UW Oshkosh

description: Genes were represented in triplicate on each array.

hyb_protocol: The labeled cDNAs were hybridized together on a Corning Epoxide slide containing the Operon E. coli Genome Oligo Set Version 1.0 printed by the Microarray and Proteomics Facility, Department of Biological Sciences, University of Alberta. The hybridizations were performed in a hybridization chamber (Corning) in a dark, humidified chamber at 67 ºC for 13 hours. The slides were then washed in pre-warmed washing buffer 2X SSC containing 0.1% SDS for 20 minutes, 2X SSC for 20 minutes, and 0.2X SSC for 20 minutes.

scan_protocol: The arrays were scanned with a Versarray ChipReader (BioRad) with laser power at 75%, photomultiplier tube (PMT) sensitivity at 800 V, and detector gain at 1.

data_processing: Spot intensities and locations were determined using TIGR Spotfinder, Version 3.1.1. All subsequent analyses were performed using the ma-anova package in the open-source statistical software package, R (www.r-project.org), Version 2.4.1. The data were normalized using the regional lowess method.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli, 15 minutes, 5 µM cadmium, pH 5

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy 3 according to the 3DNA Array 900MPX kit manufacturer’s protocols (Genisphere).

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells.

extract_protocol: RNA was extracted and purified using a Masterpure RNA purification kit (Epicentre Technologies).

tag: MG1655 strain of E. coli K-12

source_name: E. coli, 15 minutes, 5 µM cadmium, pH 7

label_protocol: Total RNA was reverse transcribed with random primer mix and labeled with Cy 5 according to the 3DNA Array 900MPX kit manufacturer’s protocols (Genisphere).

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells.


title: SBT_NS16

description: Gene expression data

source_name: SBT, patient 150


title: E. coli 15 minute pH only dye swap treatment

source_name: E. coli, 15 minutes, no cadmium, pH 5

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells.

source_name: E. coli, 15 minutes, no cadmium, pH 7

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7. The cultures were incubated at 25 °C for 15 minutes with manual rotations of the flasks once per minute to resuspend the cells.


title: SCA1_NS09

description: Gene expression data

source_name: SCA1, patient 143


title: E. coli 5 minute pH only dye swap treatment

source_name: E. coli, 5 minutes, no cadmium, pH 5

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.

source_name: E. coli, 5 minutes, no cadmium, pH 7

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.


title: SCA1_NS04

description: Gene expression data

source_name: SCA1, patient 132


title: Normal tissue for ID_003

description: no additional information

tag: Patient_ID = ID_003

tag: Sex = M

tag: Position = Right

tag: Pathology = well differentiated adenocarcinoma

tag: Duke's_grade = B

tag: Lymph_node_metastasis = No

tag: MSI = No

tag: Observation_(days) = 1670

tag: Censor = Yes


title: E. coli 5 minute 5 µM cadmium dye swap treatment

source_name: E. coli, 5 minutes, 5 µM cadmium, pH 5

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.

source_name: E. coli, 5 minutes, 5 µM cadmium, pH 7

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose. The cultures were grown on a rotary shaker (200 rpm) at 37 °C until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth). Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes. The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2. The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.


title: 7360 microaerobiosis PSY 5

source_name: B. japonicum fixJ mutant grown microaerobically

tag: Genotype

tag: Growth condition

tag: Medium


title: Cancer tissue for ID_003

description: no additional information


title: E. coli 15 minute pH only treatment


title: SBT_NS10

description: Gene expression data

source_name: SBT, patient 110

tag: Gender

tag: Tissue

tag: Classification


title: SBT_NS03

description: Gene expression data

source_name: SBT, patient 11


title: E. coli 15 minute 5 µM cadmium treatment


title: Normal tissue for ID_002

description: no additional information

tag: disease_state = Normal

tag: Patient_ID = ID_002

tag: Sex = F

tag: Observation_(days) = 1672


title: 7360 microaerobiosis PSY 4


title: Normal tissue for ID_001

description: no additional information

tag: Patient_ID = ID_001

tag: Position = Left

tag: Duke's_grade = A

tag: Observation_(days) = 1677


title: SCA1_NS12

description: Gene expression data

source_name: SCA1, patient 1


title: E. coli 5 minute pH only treatment

tag: MG1655 strain of E. coli K-12


title: 7360 microaerobiosis PSY 3


title: 7360 microaerobiosis PSY 1


title: Cancer tissue for ID_001

description: no additional information

tag: disease_state = Carcinoma

tag: Pathology = well differentiated adenocarcinoma

tag: Lymph_node_metastasis = No

tag: MSI = No


title: 7360 microaerobiosis PSY 2

tag: Genotype

tag: Growth condition

tag: Medium


title: E. coli 5 minute 5 µM cadmium treatment

data_processing: Spot intensities and locations were determined using TIGR Spotfinder, Version 3.1.1.  All subsequent analyses were performed using the ma-anova package in the open-source statistical software package, R (www.r-project.org), Version 2.4.1.  The data were normalized using the regional lowess method.

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose.  The cultures were grown on a rotary shaker (200 rpm) at 37 °C  until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth).  Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes.  The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 7 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2.  The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.

growth_protocol: E. coli was grown in M9 medium supplemented with 0.4% glucose.  The cultures were grown on a rotary shaker (200 rpm) at 37 °C  until the contents of the flask reached an OD600 of 0.3 (mid-log phase of growth).  Each culture was divided into 25 mL aliquots, transferred to four 50 mL conical tubes, and centrifuged at 2540 x g for 12 minutes.  The supernatant was decanted, and the cells were resuspended in 25 mL of M9 medium at pH 5 in the presence of 5.4 µM (1 µg/mL) total cadmium, added as CdCl2.  The cultures were incubated at 25 °C for 5 minutes with manual rotations of the flasks once per minute to resuspend the cells.


title: Cancer tissue for ID_002

description: no additional information

tag: Position = Right

tag: Duke's_grade = B

tag: Censor = Yes


title: C1 evolved YFP vs M5 3

status: Public on Aug 20 2008

city: Stanford

first: Gavin

last: Sherlock

state: CA

address: 300 Pasteur Drive

department: Genetics

institute: Stanford University

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78828.gif
Genotype: M5
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents

hyb_protocol: not provided

scan_protocol: Feature Extraction; The software Feature Extraction v 9.1.5 (Agilent Technology, Santa Clara, CA) was used extract data from the scanned images, and to normalize the data using the Spike-In controls.; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Katy,,Kao

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Saccharomyces cerevisiae

label_protocol:
not provided
Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC.  These cultures were then used to inoculate glucose-limited chemostat cultures.  Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume.  To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao

extract_protocol: not provided

source_name: YFP

label_protocol: not provided

tag: YFP


title: C1 evolved control DsRED vs GFP

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78808.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents

source_name: GFP

growth_protocol: Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC.  These cultures were then used to inoculate glucose-limited chemostat cultures.  Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume.  To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao

tag: GFP

source_name: DsRED

tag: DsRED


title: C1 evolved DsRED vs M4 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78827.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved YFP vs M3 3 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78833.gif
Genotype: M3
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control DsRED vs GFP 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78815.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M4 vs DsRED 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78819.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved DsRED vs M2 3 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78832.gif
Genotype: M2
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M1 vs GFP 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78816.gif
Genotype: M1
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved GFP vs M1 3 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78831.gif
Genotype: M1
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved GFP vs M1 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78824.gif
Genotype: M1
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved YFP vs M5 3 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78835.gif
Genotype: M5
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved DsRED vs M4 3 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78834.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M5 vs YFP

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78813.gif
Genotype: M5
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M5 vs YFP 2 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78830.gif
Genotype: M5
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: miR181b/control B cell exp2

city: Madrid

first: Almudena

middle: R.

last: Ramiro

state: Madrid

address: Calle Melchor Fernandez Almagro 3

department: Molecular Oncology

country: Spain

institute: CNIO

description: Biolgical replicate 1 of 1. Primary spleen B cell-tranduced with control-GFP and miR181b vectors selected by cell sorting after 2 days in LPS+IL-4 cultures

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 825 ng. Duration: 17 hours.Volume: 100 uL.Temperature (ºC): 65.

scan_protocol: Scanned on an G2565BA DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 9.1.3.1).

data_processing: Linear Lowess normalization performed with Agilent's Feature Extraction software.

source_name: primary spleen B cell-tranduced with control-GFP vector

label_protocol: Amount of nucleic acid labeled: 2ug.Amplification: by RNA polymerases.Commercial "Two-Color Microarray-Based Gene Expression Analysis" kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.0 Aug 2006. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Mouse primary B cells were purified from spleens of C57/BL6 mice by anti-CD43 immunomagnetic depletion (Miltenyi Biotech) and cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium

extract_protocol: Total RNA was extracted with Trizol (Invitrogen). Commercial RNeasy kit (Qiagen) was used in spin-column format following manufacturer instructions. Total RNA was analysed by Lab-chip technology on an Agilent 2100 Bioanalyzer. Samples' RNA Integrity Numbers were in the range 9.7 to 9.8

treatment_protocol: Mouse primary B cells were transduced with retroviral supernatants for 20 hours in the presence of 8 ug/ml polybrene (Sigma), 25ug/ml LPS (Sigma) and 10ng/ml IL-4 (Peprotech). GFP+ cells were isolated by cell sorting 2 days after transduction.

tag: strain

source_name: primary spleen B cell-tranduced with miR181b-GFP vector


title: C1 evolved DsRED vs M2 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78825.gif
Genotype: M2
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control GFP vs DsRED 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78822.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control YFP vs GFP

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78805.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control GFP vs YFP 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78821.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: LPS+IL-4 stimulated B cells-exp5

description:
LPS+IL4  stimulated primary mouse spleen B cell. Biological replicate 5 of 5
Activated B cells  were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences). Mouse primary B cells were cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium

hyb_protocol: Hybridizations were performed at 55°C for 17 h using the SlideHyb Microarray Hybridization buffer (Ambion).

scan_protocol: the slides were scanned in an Agilent G2565BA scanner.

data_processing: Images were then analyzed with GenePix 5.1 (Axon Instruments, Inc., Union City, CA) and the TM4 software.  Raw Intensity values were normalized by applying array Lowess normalization (MIDAS module, TM4 tools).

source_name: stimulated primary spleen B cell

label_protocol: Five micrograms of the test RNAs was labeled with fluorescent Cy3 (Amhersam, Sunnyvale), respectively using the SuperScript II RNase H Reverse Transcriptase KIT (Invitrogen, USA).

growth_protocol: Mouse primary B cells were purified from spleens of C57/BL6 mice by anti-CD43 immunomagnetic depletion (Miltenyi Biotech)

extract_protocol: Total RNA was extracted by combination of Trizol reagent (Invitrogen) without further purification. The quality of the RNA was evaluated using the BioAnalyzer system (Agilent).


title: C1 evolved control YFP vs GFP 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78814.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M3 vs YFP 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78818.gif
Genotype: M3
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control DsRED vs YFP

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78809.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M2 vs DsRED 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78817.gif
Genotype: M2
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved control YFP vs DsRED 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78823.gif
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: Non-stimulated B cells-exp5

description:
non stimulated primary mouse spleen B cell. Biological replicate 5 of 5
n/a

source_name: primary spleen B cell


title: LPS+IL-4 stimulated B cells-exp4

description:
LPS+IL4  stimulated primary mouse spleen B cell. Biological replicate 4 of 5
Activated B cells  were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences). Mouse primary B cells were cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium


title: C1 evolved M2 vs DsRED

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78811.gif
Genotype: M2
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: Non-stimulated B cells-exp3

description:
non stimulated primary mouse spleen B cell. Biological replicate 3 of 5
n/a


title: LPS+IL-4 stimulated B cells-exp3

description:
LPS+IL4  stimulated primary mouse spleen B cell. Biological replicate 3 of 5
Activated B cells  were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences). Mouse primary B cells were cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium


title: Non-stimulated B cells-exp4

description:
non stimulated primary mouse spleen B cell. Biological replicate 4 of 5
n/a


title: Non-stimulated B cells-exp1

description:
non stimulated primary mouse spleen B cell. Biological replicate 1 of 5
n/a


title: LPS+IL-4 stimulated B cells-exp2

description:
LPS+IL4  stimulated primary mouse spleen B cell. Biological replicate 2 of 5
Activated B cells  were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences). Mouse primary B cells were cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium


title: Non-stimulated B cells-exp2

description:
non stimulated primary mouse spleen B cell. Biological replicate 2 of 5
n/a


title: LPS+IL-4 stimulated B cells-exp1

description:
LPS+IL4  stimulated primary mouse spleen B cell. Biological replicate 1 of 5
Activated B cells  were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences). Mouse primary B cells were cultured in 25ug/ml LPS (Sigma), 10ng/ml IL-4 (Peprotech), 10mM Hepes (Gibco), 50uM b-mercaptoethanol (Gibco) 10% FCS RPMI medium


title: C1 evolved YFP vs M3 3

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78826.gif
Genotype: M3
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M4 vs DsRED

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78812.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M5 vs YFP 2

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78820.gif
Genotype: M5
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: C1 evolved M1 vs GFP

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78810.gif
Genotype: M1
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: miR181b/control B cell exp1 replicate2

description: Biolgical replicate 1 of 1. Primary spleen B cell-tranduced with control-GFP and miR181b vectors selected by cell sorting after 2 days in LPS+IL-4 cultures


title: NOD Aire WT MEC rep2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: Gender: male Age: 3-4.5 weeks Isolation: FACS of CD45-G8.8+Ly51intclassIIhi TECs Strain: NOD

hyb_protocol: BioArray High Yield RNA transcript labeling T7 kit (Enzo Life Sciences)

scan_protocol: Standard Affymetrix protocol

data_processing: RMA

source_name: MHC class II high thymic medullary epithelial cells, NODaireWT

label_protocol: biotin

extract_protocol: RNA by Trizol method

tag: Aire WT


title: MMCT-6 transfer clone 18G23 into TOV21G parental cell line

status: Public on Aug 19 2008

city: London

first: Ken

last: Choi

address: 46 Cleveland Street

department: Gynaecological Oncology

country: United Kingdom

institute: University College London

hyb_protocol: Test and reference DNA samples (50μl each) were combined, precipitated together with 100μg of human Cot1 DNA (1μg/μl, Invitrogen) and resuspended in 100μl of hybridization buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 4μg/μl yeast tRNA). The samples were denatured at 70oC for 15mins and pre-hybridized at 37oC for 60mins. Meanwhile, array slides were denatured at 95oC for 2mins, allowed to cool and pre-hybridized in blocking buffer (25% formamide, 0.1% SDS, 5X SSC, 1g BSA) at 42oC for 60mins. The array slides were gently washed in 0.1X SSC for 30secs and spun dry at 2000rpm for 3mins. The pre-hybridized test and reference DNA samples were applied onto cover slips and hybridized onto the array slides. The slides were then transferred into a small hybridization chamber containing Whatmann 3MM paper saturated with dH20 and incubated in a rocking hybridization oven at 42oC for 24hrs. Post hybridization, slides were washed in 2X SSC, 0.1% SDS at 45oC for 15mins, then 2X SSC, 50% formamide at 45oC for 15mins, then 2X SSC, 0.1% SDS at 45oC for 30mins and finally followed by 0.2X SSC for 15mins at room temperature. Slides were spun dry in a centrifuge for 3mins at 2000rpm and stored in a dark dry container until scanning.

scan_protocol: Hybridized microarrays were scanned using an Axon GenePix 4000B scanner at 5micron scans for both channels.

data_processing: Images were put through a data extraction program called BlueFuse (Blue Gnome, Cambridge UK) along with a clone position file. Primary data analysis and normalisation were carried out using web-based analysis tool called LIMS (Laboratory Information Management System) developed in our laboratory. The microarray data were normalised using lowess and MANOR algorithms and data points smoothed using a 1Mb window.

source_name: cell line DNA clone 18G23

label_protocol: Invitrogen: Genomic Bioprime Total kit

extract_protocol: Qiagen DNA mini kit

tag: transferred copy of chr 18

source_name: Cell line DNA TOV21G parental

tag: Recipient parental cell line


title: NOD Aire KO MEC rep2

source_name: MHC class II high thymic medullary epithelial cells, NODaireKO

tag: Aire KO


title: C1 evolved M4 vs DsRED 2 technical repeat

description:
Simple annotation: evolution, glucose
Image: http://smd.stanford.edu/MicroArray/gifs/2008-02/78829.gif
Genotype: M4
Chemostat evolution experiment C1 under glucose-limited condition at 30C.  Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents


title: MMCT-6 transfer clone 18D23 into TOV112D parental cell line

source_name: cell line DNA clone 18D23

source_name: Cell line DNA TOV112D parental


title: NOD Aire WT MEC rep3


title: NOD Aire KO MEC rep3


title: NOD Aire WT MEC rep1


title: MMCT-6 transfer clone 18G5 into TOV21G parental cell line

source_name: cell line DNA clone 18G5


title: NOD Aire KO MEC rep1


title: MMCT-6 transfer clone 18D22 into TOV112D parental cell line

source_name: cell line DNA clone 18D22


title: MMCT-6 transfer clone 6D1 into TOV112D parental cell line

source_name: cell line DNA clone 6D1

tag: transferred copy of chr 6


title: MMCT-6 transfer clone 6G115 into TOV21G parental cell line

source_name: cell line DNA clone 6G115


title: miR181b/control B cell exp1 replicate1


title: MMCT-6 transfer clone 6G3 into TOV21G parental cell line

source_name: cell line DNA clone 6G3


title: E14 Sall4 KD_rep3

city: Singapore

first: Bing

last: Lim

state: Singapore

address: 60 Biopolis Street

department: Stem Cell and Developmental Biology

country: Singapore

institute: GIS

description: no additional information

hyb_protocol: According to Illumina Protocol

scan_protocol: Illumina BeadScan

data_processing: Data were normalized with cross-correlation method; differential expression was based on the mean of the log2 fold changes (see GSE12482 supplementary files).

source_name: E14 cells with Sall4 knockdown

label_protocol: According to Illumina Protocol

growth_protocol: For microarray transcriptome profiling of Sall4- and control shRNA treated cells, cells were transfected with appropriate plasmids and cultured under puromycin selection for 3, 4 or 5 days.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and column-purified with RNeasy kits (Qiagen).

tag: Strain

value: E14 mouse ES cells


title: E14 Scrb KD_rep2

description: no additional information

source_name: E14 KD control


title: E14 Scrb KD_rep3

description: no additional information


title: E14 Scrb KD_rep1

description: no additional information


title: MMCT-6 transfer clone 6D9 into TOV112D parental cell line

source_name: cell line DNA clone 6D9


title: Xen Scrb KD_rep3

description: no additional information

source_name: Xen KD control

value: Xen cells from E4.5 blastocysts


title: E14 Sall4 KD_rep1

description: no additional information


title: Xen Scrb KD_rep1

description: no additional information


title: Xen Sall4 KD_rep2

description: no additional information

source_name: Xen cells with Sall4 knockdown


title: E14 Sall4 KD_rep2

description: no additional information


title: Xen Sall4 KD_rep3

description: no additional information


title: Xen Sall4 KD_rep1

description: no additional information


title: Trsp vs G37L

city: Bethesda

first: Dolph

middle: L

last: Hatfield

state: MD

address: 37 Convent Drive, Rm. 6032A

department: LCP

institute: NIH/NCI

description:
4 biological replicates. G37L carries two copies of the A37-->G37 mutant transgene, harvested after several passages.
Data reflect the average of the biological replicates.

hyb_protocol: Mouse oligoarrays obtained from the NCI Microarray Facility, Frederick, MD, USA, were used for the experiments. For hybridization, 10 µl each of the Cy3 and Cy5 labeled cDNAs were combined and mixed with 1 µL COT-1 DNA, preheated at 100°C for 1 min to denature the cDNA and snap cooled on ice. This mixture was added to 20 µl of 2x F-hybridization buffer (50% formamide, 10x SSC, 0.2% SDS) and pre-warmed at 42°C. The total cDNA/hybridization solution mixture was loaded onto each prehybridized slide and slides placed in hybridization chambers and incubated overnight at 42°C. Post-hybridization washing included 5 min in 2x SSC + 0.1% SDS, 5 min in 1x SSC and 5 min in 0.2x SSC, after which the slides were dried by centrifugation.

scan_protocol: Slides were scanned for each fluoroprobe at 10 µm using a Genepix 4000B (Axon Instruments). Images were analyzed with GenePix Pro 3.0 software (Axon Instruments).

data_processing:
For data processing, data files (in gpr format) and image (in jpeg format) were imported into the microarray database (mAdb) and analyzed by software tools provided by the National Cancer Institute, Center for Cancer Research in collaboration with the National Institutes of Health, Center for Information Technology, Bioinformatics and Molecular Analysis Section. The 50th Percentile (Median) method was used for normalization.
In some of the arrays, some spots could be detected only in 1 or 2 of the biological replicates; for analysis purpose, one criterion was the presence of spots in at least 3 replicates.

source_name: Liver from Trsp; wild type male, 7-8 weeks of age

label_protocol: 15 µg of total RNA in combination with oligo dT was used to generate cDNA, using the Fairplay II Microarray Labeling Kit (Stratagene) and labeled with monofunctional dye (Cy3 or Cy5) using the Fairplay coupling buffer. These reactions were carried out according to manufacturer's protocol.

growth_protocol: Mice were fed selenium sufficient diet

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions

tag: Gender

value: male

tag: Tissue

value: liver

value: B6/FVB mice

source_name: Liver from G37L; transgenic male, 7-8 weeks of age


title: Xen_rep3

description: no additional information

source_name: Xen cells wild type


title: E14_rep3

description: no additional information

source_name: ES cells wild type


title: Xen_rep1

description: no additional information


title: Xen_rep2

description: no additional information


title: Trsp vs G37H

description:
3 biological replicates. G37H carries 16 copies of the A37-->G37 mutant transgene, harvested after several passages.
Data reflect the average of the biological replicates.

source_name: Liver from G37H; transgenic male, 7-8 weeks of age


title: Trsp vs A34

description:
4 biological replicates. A34 carries two copies of the T34-->A34 mutant transgene, harvested after several passages.
Data reflect the average of the biological replicates.

source_name: Liver from A34; transgenic male, 7-8 weeks of age


title: E14_rep1

description: no additional information


title: day 12, normoxia 3

status: Public on Aug 18 2008

first: Atul

last: Butte

address: 300 Longwood Avenue

institute: Children's Hospital, Boston

description: post-natal day 12 C57Bl/6 mice, room air condition

source_name: mouse retina


title: day 10, hyperoxia 3

description: post-natal day 10 C57Bl/6 mice exposed to hyperoxia for 72 hours


title: Trsp vs DTrsp

description:
4 biological replicates. DTrsp lacks Trsp in the liver, harvested after several passages.
Data reflect the average of the biological replicates.

source_name: Liver from DTrsp; knockout male, 7-8 weeks of age


title: E14_rep2

description: no additional information


title: day 10, normoxia 2

description: post-natal day 10 C57Bl/6 mice, room air condition


title: day 10, hyperoxia 2


title: day 7 normoxia 3

description: post-natal day 7 C57Bl/6 mice, room air condition


title: day 8, normoxia 2

description: post-natal day 8 C57Bl/6 mice, room air condition


title: day 8 normoxia 3


title: day 10 normoxia 3


title: day 12, hyperoxia 2

description: post-natal day 12 C57Bl/6 mice exposed to hyperoxia for 120 hours


title: day 12, normoxia 2


title: day 7, hyperoxia 2

description: post-natal day 7 C57Bl/6 mice exposed to hyperoxia for 12 hours


title: day 12, hyperoxia 3


title: day 8, hyperoxia 3

description: post-natal day 8 C57Bl/6 mice exposed to hyperoxia for 24 hours


title: day 8, hyperoxia 2


title: day 12, normoxia 1


title: day 10, hyperoxia 1


title: day 7, hyperoxia 3


title: day 10, normoxia 1


title: day 8, normoxia 1


title: day 8, hyperoxia 1


title: day 7, hyperoxia 1


title: Liver tissue, Porcine, D_21298

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

description: High and low androstenone liver tissue samples were prepared from Duroc  boars slaughtered at approximately 100kg

hyb_protocol: The individual samples were combined with a reference sample and hybridized to porcine cDNA microarrays in a Discovery XT hybridization station (Ventana Discovery Systems,Tucson, AZ, USA). Discovery labels were printed and attached to the slides before placing the slides in the machine. The slides were then pre-hybridized at 42 ºC/32 min using 2.5 mL of a solution made of equal volumes of ChipSpread A (20 mg/mL BSA, 4x SSC, 0.5 mg/mL sodium azide) and ChipSpread B (formamide; 2 mg/mL SDS) followed by treatment with the Chip Map reagents (Chip Prep-1, -2 and - 3). The dried combined samples were resuspended in 200 µL Chiphybe80, heated at 90°C for 3 minutes, cooled to room temperature, centrifuged and carefully mixed by pipetting before loading. The slides were hybridizes at 48 ºC for 6 hours. Following hybridization, remaining oil was wiped of the backside of slides using a clean-room napkin and the slides were placed in a slide-holder from the High Throughput Wash Station (Telechem, cat.no. HTW) placed in a mTub filled with RiboWash. The slide-holder was transferred to a HTW filled with RiboWash and washed twice for 2 min with magnetic stirring at 700 rpm. The slide-holder was dipped in 2x SSC filled in a mTub, transferred to a HTW filled with 2x SSC and washed twice for 2 min with magnetic stirring at 700 rpm. The slides were then dipped 10 times in 0.1x SSC filled in a mTub and transferred to a mBox slide holder placed in a mTub filled with Elga H2O. Arrays were then dried by centrifugation (at 300 x g for 4 min placed in a mBox).

scan_protocol: Scanner: ScanArray Express HT system (Perkin Elmer), 5 µm resolution, 100 % laser power and PMT adjusted individually for each channel. Image analysis software: GenePix Pro 6 software (version 6.0.1.26, Molecular Devices Corp., CA, USA), FeatureType=Irregular Filled, BackgroundSubtraction=LocalFeature.

data_processing: Statistical analyses were carried out in R version 2.3.1 using the software package Linear Models for Microarray Analysis (Limma version 2.7.2) which is part of the Bioconductor packages. Log-transformed ratios of mean foreground intensities (not background corrected) were printtip loess normalised. The duplicate correlation function in Limma was used to consider the duplicate printing of each feature. For assessing differential expression, Limma uses linear models in combination with an empirical Bayes method to moderate the standard errors of the estimated log-fold changes. The nominal p-values were corrected for multiple testing by false discovery rates (FDR) using Benjamini and Hochberg approach. The top 1 % of the genes was considered for further analyses. The features of the arrays were mapped to a LocusLink identifier and an annotation package was built using the Bioconductor package AnnBuilder (version 1.9.14). Tests for significantly overrepresentation of GO terms (p < 0.01 and more than 10 significant genes) were conducted using the GOHyperG function of the Bioconductor package GOstats (version 1.6.0).

organism: Sus scrofa

source_name: Liver tissue, Norwegian Duroc, Low androstenone

label_protocol: 15 µg total RNA was labelled by using the Superscript Indirect cDNA Labeling System (Invitrogen) in combination with ARES cDNA labeling kits (Molecular Probes/Invitrogen) following the enclosed protocols. Spike-in RNA from the Lucidea Universal ScoreCard (Amersham Biosciences) was added to the cDNA reactions. Green spike-in RNA was added to the samples labeled with Alexa-647 and red spike-in RNA was added to the reference labeled with Alexa-555. The amino-modified and the fluorescently labelled cDNA was purified using NucleoSpin 96 Extract II PCR Clean-up kits (Macherey-Nagel, Düren, Germany).

extract_protocol: Total-RNA extractions with DNase treatment using RNeasy Midi Kit from Qiagen

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:21298

source_name: Porcine reference liver

tag: Breed

value: Danish Landrace x Hampshire, Tissue:liver


title: day 7, normoxia 1


title: Xen Scrb KD_rep2

description: no additional information


title: Liver tissue, Porcine, D_10975

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:10975


title: Liver tissue, Porcine, L_8603

description: High and low androstenone liver tissue samples were prepared from Landrace  boars slaughtered at approximately 100kg

source_name: Liver tissue, Norwegian Landrace, Low androstenone

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8603


title: Liver tissue, Porcine, D_4521

source_name: Liver tissue, Norwegian Duroc, High androstenone

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:4521


title: Liver tissue, Porcine, L_12618

source_name: Liver tissue, Norwegian Landrace, High androstenone

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:12618


title: Liver tissue, Porcine, L_12145

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:12145


title: Liver tissue, Porcine, D_26536

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:26536


title: Liver tissue, Porcine, L_25728

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:25728


title: Liver tissue, Porcine, L_24216

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:24216


title: Liver tissue, Porcine, D_13581

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:13581


title: Liver tissue, Porcine, D_10983

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:10983


title: Liver tissue, Porcine, L_19125

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:19125


title: Liver tissue, Porcine, L_24406

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:24406


title: Liver tissue, Porcine, D_7671

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:7671


title: Liver tissue, Porcine, L_6286

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:6286


title: Liver tissue, Porcine, L_11457

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:11457


title: Liver tissue, Porcine, L_22573

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:22573


title: Liver tissue, Porcine, L_35221

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:35221

value: Danish Landrace x Hampshire, Tissue:liver


title: Liver tissue, Porcine, D_4311

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:4311


title: Liver tissue, Porcine, L_8282

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8282


title: Liver tissue, Porcine, D_5980

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:5980


title: Liver tissue, Porcine, D_23810

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:23810


title: Liver tissue, Porcine, D_20324

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:20324


title: day 7, normoxia 2


title: day 12, hyperoxia 1


title: Liver tissue, Porcine, L_15140

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:15140


title: Liver tissue, Porcine, D_5387

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:5387


title: Liver tissue, Porcine, D_30688

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:30688


title: Liver tissue, Porcine, L_12299

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:12299


title: Liver tissue, Porcine, L_17811

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:17811


title: Liver tissue, Porcine, D_1172

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:1172


title: Liver tissue, Porcine, D_19986

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:19986


title: Liver tissue, Porcine, L_17074

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:17074


title: Liver tissue, Porcine, L_11444

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:11444


title: Liver tissue, Porcine, L_17805

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:17805


title: Liver tissue, Porcine, L_15489

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:15489


title: Liver tissue, Porcine, D_35222

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:35222

value: Danish Landrace x Hampshire, Tissue:liver


title: Liver tissue, Porcine, L_483

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:483


title: Liver tissue, Porcine, D_24835

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:24835


title: Liver tissue, Porcine, L_7515

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:7515


title: Liver tissue, Porcine, D_11425

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:11425


title: Liver tissue, Porcine, L_20857

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:20857


title: Liver tissue, Porcine, D_4979

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:4979


title: Liver tissue, Porcine, D_3529

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:3529


title: Liver tissue, Porcine, D_7881

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:7881


title: Liver tissue, Porcine, L_8305

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8305


title: Liver tissue, Porcine, L_8285

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8285


title: Liver tissue, Porcine, L_24834

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:24834


title: Liver tissue, Porcine, L_25714

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:25714


title: Liver tissue, Porcine, D_24232

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:24232


title: Liver tissue, Porcine, L_8308

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8308


title: Liver tissue, Porcine, L_18926

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:18926


title: Liver tissue, Porcine, D_4039

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:4039


title: Liver tissue, Porcine, L_23815

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:23815

value: Danish Landrace x Hampshire, Tissue:liver


title: Liver tissue, Porcine, L_8023

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8023


title: Liver tissue, Porcine, D_24408

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:24408


title: Liver tissue, Porcine, L_15762

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:15762


title: Liver tissue, Porcine, D_35211

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:35211


title: Liver tissue, Porcine, D_14532

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:14532


title: Liver tissue, Porcine, L_5386

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:5386


title: Liver tissue, Porcine, L_3010

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:3010


title: Liver tissue, Porcine, L_18925

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:18925


title: Liver tissue, Porcine, D_30681

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:30681


title: Liver tissue, Porcine, L_5693

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:5693


title: Liver tissue, Porcine, D_5992

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:5992


title: Liver tissue, Porcine, D_12621

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:12621


title: Liver tissue, Porcine, L_18565

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:18565


title: Liver tissue, Porcine, D_3022

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:3022


title: Liver tissue, Porcine, L_1395

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:1395


title: Liver tissue, Porcine, D_8862

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:8862


title: Liver tissue, Porcine, L_3009

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:3009

value: Danish Landrace x Hampshire, Tissue:liver


title: Liver tissue, Porcine, L_9128

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:9128


title: Liver tissue, Porcine, L_12623

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:12623


title: Liver tissue, Porcine, D_20864

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:20864


title: Liver tissue, Porcine, D_4531

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:4531


title: Liver tissue, Porcine, L_11449

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:11449


title: Liver tissue, Porcine, L_7041

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:7041


title: Liver tissue, Porcine, D_20310

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:20310


title: Liver tissue, Porcine, L_5676

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:5676


title: Liver tissue, Porcine, L_21081

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:21081


title: Liver tissue, Porcine, D_9120

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:9120


title: Liver tissue, Porcine, D_19385

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:19385


title: Liver tissue, Porcine, L_11815

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:11815


title: Liver tissue, Porcine, L_8306

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8306


title: Liver tissue, Porcine, L_5394

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:5394


title: Liver tissue, Porcine, D_30241

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:30241


title: Liver tissue, Porcine, D_9095

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:9095


title: Liver tissue, Porcine, D_40013

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:40013

value: Danish Landrace x Hampshire, Tissue:liver


title: Liver tissue, Porcine, D_13538

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:13538


title: Liver tissue, Porcine, D_826

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:826


title: Liver tissue, Porcine, D_5419

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:5419


title: Liver tissue, Porcine, D_5397

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:5397


title: Liver tissue, Porcine, D_5407

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:5407


title: Liver tissue, Porcine, D_17090

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:17090


title: Liver tissue, Porcine, L_18514

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:18514


title: Liver tissue, Porcine, D_13120

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:13120


title: Liver tissue, Porcine, L_11814

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:11814


title: Liver tissue, Porcine, L_474

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:474


title: SB10C_alphaCBnGalNAc_1

city: Berlin

first: Andreas

last: Klein

address: Charitéplatz 1

department: Institute of Biochemistry

institute: Charité (CCO)

description: PC/AA/C1/SB10C cells treated with alphaCBnGalNAc.

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 2.0 Array. Washing steps for the chip, staining with streptavidin-phycoerythrin and signal-amplification were performed according to the manufacturer’s instructions.

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with GeneChip Scanner 3000.

data_processing: The raw experimental microarray data were normalized with the GeneChip operating software (GCOS, Affymetrix). Further analyses were performed with the software “CorrXpression”.

label: Biotin

source_name: Colon cancer cell line, alphaCBnGalNAc

label_protocol: cRNA was amplified from 5 µg of total RNA using the standard Affymetrix procedure.

extract_protocol: RNAzol extraction of total RNA was performed according to the manufacturer's instructions (PeQLab, Biotechnology) and treated with RNase-free DNase (DNA-free, Ambion, USA).

treatment_protocol: SB10C cells were seeded at 1x10e6 per four mls of medium and cultured in a 20% FBS standard growth medium with of 0.2U/ml insulin (conditioned medium) for three days. Then, cells were incubated in the presence or absence of each of the inhibitors at a concentration of 0.5mM, in either standard growth or conditioned medium and seeded after 4 days.

tag: Human colon cancer cell line

tag: O-glycan inhibitor


title: SB10C_alphaOBnGalN3_2

description: PC/AA/C1/SB10C cells treated with alphaOBnGalN3.

source_name: Colon cancer cell line, alphaOBnGalN3


title: SB10C_alphaCBnGalNAc_2

hyb_protocol: Following fragmentation, the cRNA was hybridized for 16 hr at 45C on GeneChip® Human Genome U133A 2.0 Array. Washing steps for the chip, staining with streptavidin-phycoerythrin, and signal-amplification were performed according to the manufacturer’s instructions.


title: Liver tissue, Porcine, L_12159

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:12159


title: Liver tissue, Porcine, D_2048

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:2048


title: Liver tissue, Porcine, D_25924

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:25924


title: Liver tissue, Porcine, D_33524

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:33524


title: Liver tissue, Porcine, D_28300

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:28300


title: Liver tissue, Porcine, L_23172

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, High androstenone, biomat-id:23172


title: Liver tissue, Porcine, D_23833

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:23833

value: Danish Landrace x Hampshire, Tissue:liver


title: HT3 delta PsbV

type: protein

city: Saint Louis

first: Eric

middle: Agnew

last: Welsh

state: MO

address: One Brookings Drive; Campus Box 1137

department: Biology

institute: Washington University in Saint Louis

description:
PSII Preparation:
PSII was isolated from HT3, deltaPsbV HT3, deltaPsbQ HT3, and deltaPsbP HT3 strains as described previously . HT3 indicates the 6-His tagged CP47 used to affinity purify the complex . The final eluate from a Ni-NTA Agarose (Qiagen, Inc., Valencia, CA) column was suspended in 50 mM MES-NaOH pH 6.0, 10 mM CaCl2, 25% glycerol with 0.04% dodecyl maltoside. Chlorophyll concentrations were determined by methanol extraction and absorbance at 652 and 665 nm in a DW2000 spectrophotometer (SLM-Aminco, Urbana, IL) .
AMT Peptide Identification:
PSII preparations of approximately 1 mg protein were sent to Pacific Northwest National Laboratory (PNNL) for protein identification. The PSII samples were denatured by addition of equal volumes of 7 M urea, 2 M thiourea, and 1% CHAPS in 50 mM ammonium bicarbonate, pH 7.8 and then reduced with DTT to a final concentration of 5mM. CaCl2 was added to a final concentration of 1 mM.
Samples were digested by the addition of sequencing grade modified trypsin (Promega, Madison, WI), using a ratio of 1:100 (wt/wt) protease to protein sample and incubated 4 hours at 37oC. Digests were desalted using Supelco Superclean SCX tubes (St. Louis, MO) with a Supelco vacuum manifold. The pH of each digestion was adjusted to 3.5 by addition of dilute formic acid. The SCX resin was conditioned with acetonitrile followed by 0.5 column volume (cv) 1M sodium formate. The column was washed with 2 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5 and the resin was re-equilibrated with 1 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptide mixtures were loaded onto the resin and washed with 3 cv of 5% acetonitrile in 10 mM ammonium formate, pH 3.5. Peptides were eluted with 1 cv of 25% acetonitrile in 500 mM ammonium acetate, pH 8.5, followed by 0.5 cv of 100% acetonitrile. Eluted peptides were concentrated via Speedvac (ThermoSavant, San Jose, CA) to protein concentrations of 1.0 mg/mL, as determined by BCA assay (Pierce, Rockford, IL).
Peptides were putatively identified using a capillary LC system, of a pair of model 100mL 100DM syringe pumps (Teledyne-Isco, Lincoln, NE), a series D controller (Teledyne-Isco, Lincoln, NE) and an in-house manufactured mixer, capillary column selector, and sample loop. Separations were achieved using a 5000 psi reversed-phase in-house packed capillary (150 um i.d., 360 um o.d., 60 cm long; Polymicro Technologies, Phoenix, AZ) by using an exponential gradient of 2 mobile-phase solvents consisting of 0.2% acetic acid and 0.05% trifluroacetic acid (TFA) in water and 0.1% TFA in 90% acetonitrile. Flow through the capillary HPLC column was ?1.8 uL/min when equilibrated to 100% mobile-phase 0.2% acetic acid and 0.05% TFA.
For each HPLC sample, 10 ug was infused into a LCQ conventional ion trap MS (ThermoFinnigan, San Jose, CA) operating in a data dependent MS/MS mode over a 400 to 2000 m/Z range. For each cycle, the 3 most abundant ions from MC analysis were selected for MS/MS analysis by using a collision energy setting of 45%. Dynamic exclusion was used to discriminate against previously analyzed ions. The collision induced dissociation spectra from the conventional ion trap mass spectrophotometer were analyzed using SEQUEST  and the genome sequence of Synechocystis 6803. PMT identifications were made based on a SEQUEST cross correlation (Xcorr) score ? 2.0, regardless of charge or mass.
Using the same LC conditions, 5 ug of each sample analyzed in the ion trap was then analyzed in duplicate or triplicate by FTICR-MS. The FTICR mass spectrometers use ESI interfaced with an electrodynamic ion funnel assembly coupled to a radio frequency quadropole for collisional ion focusing and highly efficient ion accumulation and transport to a cylindrical FTICR for cell analysis .
The resultant FTICR data was processed using the PRISM Data Analysis system, a series of software tools developed in-house. First the MS data was de-isotoped, giving the monoisotopic mass, charge, and intensity of the major peaks in each mass spectrum. Following this, the data was examined in a two-dimensional fashion to find groups of mass spectral peaks that were observed in sequential spectra. Each group, known as a unique mass class (UMC), has a median mass, central normalized elution time (NET), and abundance estimate, computed by summing the intensities of the MS peaks that compromise the UMC.
The identity of each UMC was determined by comparing the mass and NET of each UMC with the mass and NET’s of the 4423 PMT’s in the Synechocystis 6803 AMT database (generated using the peptides observed from 23 LC/MS/MS). Search tolerances were ± 6 ppm for the mass and ±5% of the total run time for the elution time.

data_processing: A threshold of 0.18 units was applied to the peptide abundance data to discard all measurements below the chosen noise threshold. Replicate data for each peptide were averaged, and the average abundances used to calculate log2 (mutant / HT3 wild type) ratios for each peptide. Peptides that were not present in at least two replicates for both HT3 wild type and mutant were discarded. The remaining peptides were then used to calculate average log2 ratios for their respective proteins. Standard errors were calculated for the replicates and propagated through all calculations.

molecule: protein

organism: Synechocystis sp. PCC 6803

source_name: HT3 delta PsbV

growth_protocol: All chemicals used for media and other experiments are from Sigma (St. Louis, MO) unless otherwise noted. Synechocystis cultures were grown at 30oC under 20 umol photons m-2 s-1 white fluorescent light in TES buffered BG11 medium  on a rotary shaker at 110 rpm. Stock cultures were maintained on solid medium (BG11 supplemented with 1.5% (w/v) agar), and used to inoculate liquid cultures for each experiment. When needed for mutants, growth medium was supplemented with 10 ug/mL spectinomycin, 2 ug/mL gentamycin, and 10 ug/mL chloramphenicol. Cyanobacterial cell growth was monitored by measuring light scattering at 730 nm on a uQuant microplate spectrophotometer (Bio-Tek Instruments, Inc., Toronto, Canada). To create a putative mass tag (PMT) of Synechocystis proteins, cultures were grown in complete BG11 as well as in media deplete of nitrogen, phosphorous, sulfur, or iron; media containing sodium chloride, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), or carbon dioxide; or cultures were subjected to heat or cold shock.

tag: PSII complex from HT3 delta PsbV mutant strain

source_name: HT3 wild type

growth_protocol: as above

tag: PSII complex from HT3 wild type strain


title: Liver tissue, Porcine, L_8017

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:8017


title: SB10C_alphaOBnGalNAc_2

description: PC/AA/C1/SB10C cells treated with alphaOBnGalNAc.

source_name: Colon cancer cell line, alphaOBnGalNAc


title: HT3 delta PsbQ

source_name: HT3 delta PsbQ

tag: PSII complex from HT3 delta PsbQ mutant strain


title: Liver tissue, Porcine, D_3020

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, Low androstenone, biomat-id:3020


title: SB10C_alphaOBnGalN3_1


title: Liver tissue, Porcine, L_7071

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:7071


title: Liver tissue, Porcine, L_823

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:823


title: Liver tissue, Porcine, D_20777

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:20777


title: SB10C_Control_2

description: PC/AA/C1/SB10C cells under standard culture conditions.

source_name: Colon cancer cell line, no inhibitor

tag: Control


title: Liver tissue, Porcine, D_4787

value: male, Tissue:porcine liver tissue, Breed:Norwegian Duroc, High androstenone, biomat-id:4787


title: Liver tissue, Porcine, L_7059

value: male, Tissue:porcine liver tissue, Breed:Norwegian Landrace, Low androstenone, biomat-id:7059


title: SB10C_alphaOBnGalNAc_1


title: HT3 delta PsbP

source_name: HT3 delta PsbP mutant

tag: PSII complex from HT3 delta PsbP mutant strain